annotate VCF files for poly repeats
meta{:bash}
:map
Groovy Map containing VCF information
vcf{:bash}
:file
Groovy Map containing reference genome information for vcf
*.{vcf,bcf,vcf.gz,bcf.gz}
tbi{:bash}
Alternative VCF file index
*.tbi
regions_file{:bash}
Regions file
meta2{:bash}
Groovy Map containing fasta information
fasta{:bash}
Groovy Map containing reference genome information for fai reference fasta file
*.fasta
meta3{:bash}
Groovy Map containing fasta.fai information
fai{:bash}
Groovy Map containing reference genome information for fai
*.fasta.fai
meta4{:bash}
Groovy Map containing fasta.dict information
dict{:bash}
Groovy Map containing reference genome information for GATK sequence dictionary
*.dict
Groovy Map containing VCF information e.g. [ id:‘test’, single_end:false ]
*.${extension}{:bash}
VCF filtered output file
*.tbi{:bash}
csi{:bash}
*.csi{:bash}
Default VCF file index
*.csi
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Java utilities for Bioinformatics.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
